

WebLogo Release Notes

WebLogo Release Notes


3.2 (2012-01-30) [Gavin Crooks, David Sivak]

* Graphical interface now accepts transfac format motif files.
* New output format option: SVG (Scalable Vector Graphics)
* Miscellaneous minor bug fixes and refactoring.


3.1 (2011-08-16) [Gavin Crooks, David Sivak]

Mostly bug fixes, code improvements and minor user enhancements.

* Command line: Add parsing of transfac PWM files
* Command line: Add reverse and complement transformations
* Improve clustal file parsing
* Currently compatible with python 2.5, 2.6 and 2.7
* Deprecate support for python 2.3 and 2.4
* Migrate corebio library into weblogo for easier maintenance and development.
* Add new annotate option for custom annotation line
* Miscellaneous minor bug fixes and refactoring.

* Incorporates bug fixes and feedback from Gavin Crooks, John Gilman, 
Kevin Schutz and Perry Evan.



3.0 (2008-10-14) [GEC]

A significant update of WebLogo.

New and improved feature include:

* Simplified GUI. More useful options, less obscure options that are rarely
  used.
* Several choices of unit including bits and nats, and corresponding energy 
  measures such as kJ/mol.
* Error bars are smaller and more discrete.
* The size of logo stacks is consistent (Does not change with sequence length.)
* The width of the characters in a stack are scaled by the fraction of non-gaps.
  Therefore gappy columns are visually less important than columns with gaps.
* Three standard logo sizes.
* Can now read many multiple sequence alignment formats, including
  CLUSTALW, FASTA, plain flatfile, MSF, NBRF, PIR, NEXUS and PHYLIP.
* High resolution PNG output.
* New, rational, easy to use command line client.
* Python based API library.
* New color schemes, including Watson-Crick pairing, hydrophobicity and charge.
* I (Isolucine) now shows crossbars, so that the letter is distinguishable
  from a line.
* Colors can be specified using CSS2 syntax.
* Optional figure label.
* Conservation is now calculated as the Bayesian posterior mean relative
  entropy. (This is the most significant change scientifically. The math
  needed to get this right is very interesting.)
* Similarly, we now display Bayesian 95% confidence intervals for error bars.
* Compositional adjustment.

* Includes contributions from Clare Gollnick, David Ding, John Gilman.
* Incorporates bug fixes and feedback from John Reid, Gordon Robertson, 
  Eric Odell, Krisztina Gabor, ...
* Incorporates or adapts ideas and code from Gary Hon, Steven Brenner,      
     John-Marc Chandonia, Liana Lareau, Ed Green, James Casbon, Jeffrey Chang,
     Frank Kauff, Cymon J. Cox,   ...




-----------------------------------------------------------------------

2.8.2 (2005-09-08)  [LL, GEC]
  Various Bug fixes:
    * Fixed Yellow (Was orange)
    * Various improvements in handling malformed input.
    * Fixed the fineprint checkbox option, which was stuck on.
    * Renamed "Uniform Height Logo" option to a more descriptive
      "Frequency Plot", and removed deceptive y-axis.

2.8.1 (2004-10-18) (Minor bug fix release) [GEC]

Bug fixes:
 * Made weblogo compatibly with ghostscript version 8.1x.
    This release is known to work with ghostscript version 7.05, 8.00 & 8.14

Kudos for bug reports and suggestions to:
 * Lei Shen   


2.8 (2004-10-01) [GEC]

Bug fixes:
 * Fixed another form data parsing bug whose only apparent effect was to
    fill up the webserver's error log.
 * Fixed an issue with using double slashes in weblogo's url.

Kudos for bug reports and suggestions to:
 * Eric Odell    
 * Scot Wolfe
 * Alban Mancheron
 * Ed Green

 
2.7 (2004-06-09)  [GEC]

Bug fixes :
 * Fixed logo.cgi's parsing of checkbox form data.
 
Kudos for bug reports and suggestions to:
 * Eric Odell


2.6 (2004-03-15)  [GEC, GH]

Bug fixes:
 * Resolved an issue with hard coded paths within the 
    seqlogo command line client
 * Improved the parsing of clustalw files

Kudos for bug reports and suggestions to:
 * Allen Liu
 * Guo Anyaun
 * Harald Weber


2.5 (2004-02-19)  [GEC, GH]

New features and enhancements :
 * Added multiline logos.


2.4 (2004-01-29) [GEC, GH]

New features and enhancements :
 * Added file upload for sequence data.
 * Updated main page to reflect updated publication status


2.3 (2003-11-03) [GEC, GH]

New features and enhancements
 * Added ability to parse CLUSTALW and flat file multiple sequence
   alignment formats.

Bug fixes:
 * Antialiasing PNGs now works with recent versions of ghostscript
 * Can now change output file type when using Mozilla.


Kudos for bug reports and suggestions to:
 * Stefanie Lager
 * Ed Green
 * Michael Galperin 


2.2 (2003-08-01) [GEC, GH]

Several minor bug fixes and changes to the web pages.
 * Fixed various buggy command line options
 * A request for an empty yaxis label is now respected
 * Fixed a major bug in temporary file name assignment
   that prevented weblogo from running on some unix variants

New features and enhancements 
 * Made error bars darker
 * Added option to control distance between tic marks

Kudos for bug reports and suggestions to
 * Stefanie Lager
 * Arlin Stoltzfus
 * JP Cartailler  
 * Peter G. Warren


2.1 (2003-01-08) [GEC]

Several minor bug fixes and changes to the web pages.

2.0 (2002) [GEC, GH, JMC, SEB]

This second version of WebLogo is a complete rewrite of both
the user interface and the backend. Many new features and
options have been provided.

1.0 (1995) [SEB]

The original version of WebLogo was written in 1995 by Steven 
Brenner, and was hosted by the School of Biological Science, 
University of Cambridge


WebLogo change log
-----------------------     
+ New feature
* Changed/Improved feature
! Fixed bug
- Removed feature

Versions : major.minor.patch. 

The WebLogo Team 
------------------

LL:  Liana Lareau
GEC: Gavin E. Crooks
GH:  Gary Hon
JMC: John-Marc Chandonia
SEB: Steven E. Brenner 




